High-resolution array CGH increases heterogeneity tolerance in the analysis of clinical samples

Recent advances in array comparative genomic hybridization (array CGH) technology are revolutionizing our understanding of tumor genomes. Marker-based arrays enable rapid survey at megabase intervals, while tiling path arrays examine the entire genome in unprecedented detail. Tumor biopsies are typically small and contain infiltrating stromal cells, requiring tedious microdissection. Tissue heterogeneity is a major barrier to high-throughput profiling of tumor genomes and is also an important consideration for the introduction of array CGH to clinical settings. We propose that increasing array resolution will enhance detection sensitivity in mixed tissues and as a result significantly reduce microdissection requirements. In this study, we first simulated normal cell contamination to determine the heterogeneity tolerance of array CGH and then validated this detection sensitivity model on cancer specimens using the newly developed submegabase resolution tiling-set (SMRT) array, which spans the human genome with 32,433 overlapping BAC clones.     

Persistence of Tandem Arrays: Implications for Satellite and Simple-Sequence Dnas

Recombination processes acting on tandem arrays are suggested here to have probable intrinsic biases, producing an expected net decrease in array size following each event, in contrast to previous models which assume no net change in array size. We examine the implications of this by modeling copy number dynamics in a tandem array under the joint interactions of sister-strand unequal crossing over (rate gamma per generation per copy) and intrastrand recombination resulting in deletion (rate epsilon per generation per copy). Assuming no gene amplification or selection, the expected mean persistence time of an array starting with z excess copies (i.e., array size z + 1) is z(1 + gamma/epsilon) recombinational events. Nontrivial equilibrium distributions of array sizes exist when gene amplification or certain forms of selection are considered. We characterize the equilibrium distribution for both a simple model of gene amplification and under the assumption that selection imposes a minimal array size, n. For the latter case, n + 1/alpha is an upper bound for mean array size under fairly general conditions, where alpha(= 2 epsilon/gamma) is the scaled deletion rate. Further, the distribution of excess copies over n is bounded above by a geometric distribution with parameter alpha/(1 + alpha). Tandem arrays are unlikely to be greatly expanded by unequal crossing over unless alpha much less than 1, implying that other mechanisms, such as gene amplification, are likely important in the evolution of large arrays. Thus unequal crossing over, by itself, is likely insufficient to account for satellite DNA.     

SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays

We developed a new platform for genome-wide gene expression analysis in any eukaryotic organism, which we called SuperSAGE array. The SuperSAGE array is a microarray onto which 26-bp oligonucleotides corresponding to SuperSAGE tag sequences are directly synthesized. A SuperSAGE array combines the advantages of the highly quantitative SuperSAGE expression analysis with the high-throughput microarray technology. We demonstrated highly reproducible gene expression profiling by the SuperSAGE array for 1,000 genes (tags) in rice. We also applied this technology to the detailed study of expressed genes identified by SuperSAGE in Nicotiana benthamiana, an organism for which sufficient genome sequence information is not available. We propose that the SuperSAGE array system represents a new paradigm for microarray construction, as no genomic or cDNA sequence data are required for its preparation.     

The Evolution of Tandemly Repetitive DNA: Recombination Rules

Variable numbers of tandem repeats (VNTRs), which include hypervariable regions, minisatellites and microsatellites, can be assigned together with satellite DNAs to define a class of noncoding tandemly repetitive DNA (TR-DNA). The evolution of TR-DNA is assumed to be driven by an unbiased recombinational process. A simulation model of unequal exchange is presented and used to investigate the evolutionary persistence of single TR-DNA lineages. Three different recombination rules are specified to govern the expansion and contraction of a TR-DNA lineage from an initial array of two repeats to, finally, a single repeat allele, which cannot participate in a misalignment and exchange process. In the absence of amplification or selection acting to bias array evolution toward expansion, the probability of attaining a target array size is a function only of the initial number of repeats. We show that the proportions of lineages attaining a targeted array size are the same irrespective of recombination rule and rate, demonstrating that our simulation model is well behaved. The time taken to attain a target array size, the persistence of the target array, and the total persistence time of repetitive array structure, are functions of the initial number of repeats, the rate of recombination, and the rules of misalignment preceding recombinational exchange. These relationships are investigated using our simulation model. While misalignment constraint is probably greatest for satellite DNA it also seems important in accounting for the evolution of VNTR loci including minisatellites. This conclusion is consistent with the observed nonrandom distributions of VNTRs and other TR-DNAs in the human genome.     

Dynamic microtubule-dependent interactions position homotypic neurones in regular monolayered arrays during retinal development

In the vertebrate retina cell layers support serial processing, while monolayered arrays of homotypic neurones tile each layer to allow parallel processing. How neurones form layers and arrays is still largely unknown. We show that monolayered retinal arrays are dynamic structures based on dendritic interactions between the array cells. The analysis of three developing retinal arrays shows that these become regular as a net of dendritic processes links neighbouring array cells. Molecular or pharmacological perturbations of microtubules within dendrites lead to a stereotyped and reversible disruption of array organization: array cells lose their regular spacing and the arrangement in a monolayer. This leads to a micro-mechanical explanation of how monolayers of regularly spaced 'like-cells' are formed.     

Application of a superword array in genome assembly

We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array. We describe simple algorithms for constructing and using a superword array to find pairs of sequences that share a unique superword. The algorithms are implemented in a genome assembly program called PCAP.REP for computation of overlaps between reads. Experimental results produced by PCAP.REP and PCAP on a whole-genome dataset show that PCAP.REP produced a more accurate and contiguous assembly than PCAP.     

Does the aquatic invertebrate nipple array prevent bubble adhesion? An experiment using nanopillar sheets

The nipple array is a submicrometre-scale structure found on the cuticle surfaces of various invertebrate taxa. Corneal nipples are an antiglare surface in nocturnal insects, but the functional significance of the nipple array has not been experimentally investigated for aquatic organisms. Using nanopillar sheets as a mimetic model of the nipple array, we demonstrated that significantly fewer bubbles adhered to the nanopillar surface versus a flat surface when the sheets were hydrophilic. Many more bubbles adhered to the hydrophobic surface than the hydrophilic surfaces. Bubbles on the body surface may cause buoyancy problems, movement interference and water flow occlusion. Here, bubble repellence is proposed as a function of the hydrophilic nipple array in aquatic invertebrates and its properties are considered based on bubble adhesion energy.     

The Sec-1 locus on the short arm of chromosome 1R of rye (Secale cereale)

This paper describes a detailed sequence analysis of the ω-secalin gene array at theSec-1 locus on the short arm of chromosome 1 of rye. The analysis shows that the genes are separated by 8 kb of spacer sequence and that the gene/spacer units are arranged in a head to tail fashion. The boundaries of the array are identified, and a fragment containing the majority of the genes in the array is separated by PFG analysis. The sequence data of one 9.2 kb gene unit have been determined, and because of the similarity of the gene units within the array these data provide a detailed sequence analysis of 140 kb of theSec-1 locus. Fluorescence in situ hybridization, using lambda clones isolated for the structural analysis, identifies the position of the array on the rye chromosomes relative to the 5S rRNA genes. Edited by: W. Hennig     

Concerted evolution of the tandem array encoding primate U2 snRNA (the RNU2 locus) is accompanied by dramatic remodeling of the junctions with flanking chromosomal sequences.

The genes encoding primate U2 snRNA are organized as a nearly perfect tandem array (the RNU2 locus) that has been evolving concertedly for >35 Myr since the divergence of baboons and humans. Thus the repeat units of the tandem array are essentially identical within each species, but differ between species. Homogeneity is maintained because any change in one repeat unit is purged from the array or fixed in all other repeats. Intriguingly, the cytological location of RNU2 has remained unchanged despite concerted evolution of the tandem array. We had found previously that junction sequences between the U2 tandem array and flanking DNA were subject to remodeling over a region of 200-300 bp during the past 5 Myr in the hominid lineage. Here we show that the junctions between the U2 tandem array and flanking DNA have undergone dramatic rearrangements over a region of 1 to >10 kbp in the 35 Myr since divergence of the Old World Monkey and hominid lineages. We argue that these rearrangements reflect the high level of genetic activity required to sustain concerted evolution, and propose a model to explain why maintenance of homogeneity within a tandemly repeated multigene family would lead to junctional diversity.     

Sensitive chemical sensor array based on nanozymes for discrimination of metal ions and teas

Tea, originating from China, is an important part of Chinese traditional culture. There are different qualities of and producing areas for tea on the market, therefore it is necessary to discriminate between teas in a fast and accurate way. In this study, a chemical sensor array based on nanozymes was developed to discriminate between different metal ions and teas. The indicators for the sensor array are three kinds of nanozymes mimicking laccase (Cu‐ATP, Cu‐ADP, Cu‐AMP). The as‐developed sensor array successfully discriminated 12 metal ions and the detection limit was as low as 0.01 μM. The as‐developed sensor array was also able to discriminate tea samples. Different kinds of tea samples appeared in different areas in the canonical score plot with different response patterns. Furthermore, in a blind experiment, we successfully discriminated 12 samples with a 100% accuracy. This sensor array integrates chemistry and food science together, realizing the simultaneous detection of several kinds of teas using a sensitive method. The as‐developed sensor array would have an application in the tea market and provide a fast and easy method to discriminate between teas.     

Linkage disequilibrium among commonly genotyped SNP variants detected from bull sequence,

Genomic prediction utilizing causal variants could increase selection accuracy above that achieved with SNPs genotyped by currently available arrays used for genomic selection. A number of variants detected from sequencing influential sires are likely to be causal, but noticeable improvements in prediction accuracy using imputed sequence variant genotypes have not been reported. Improvement in accuracy of predicted breeding values may be limited by the accuracy of imputed sequence variants. Using genotypes of SNPs on a high‐density array and non‐synonymous SNPs detected in sequence from influential sires of a multibreed population, results of this examination suggest that linkage disequilibrium between non‐synonymous and array SNPs may be insufficient for accurate imputation from the array to sequence. In contrast to 75% of array SNPs being strongly correlated to another SNP on the array, less than 25% of the non‐synonymous SNPs were strongly correlated to an array SNP. When correlations between non‐synonymous and array SNPs were strong, distances between the SNPs were greater than separation that might be expected based on linkage disequilibrium decay. Consistently near‐perfect whole‐genome linkage disequilibrium between the full array and each non‐synonymous SNP within the sequenced bulls suggests that whole‐genome approaches to infer sequence variants might be more accurate than imputation based on local haplotypes. Opportunity for strong linkage disequilibrium between sequence and array SNPs may be limited by discrepancies in allele frequency distributions, so investigating alternate genotyping approaches and panels providing greater chances of frequency‐matched SNPs strongly correlated to sequence variants is also warranted. Genotypes used for this study are available from https://www.animalgenome.org/repository/pub/ ;USDA2017.0519/.     

Determination of frictional conditions between electrode array and endosteum lining for use in cochlear implant models

Frictional conditions between the electrode array (in cochlear implants) and the endosteum lining covering the walls of the interior scala tympani structure strongly influence the sliding behaviour of the electrode array. Friction coefficients, determined by a simple but effective method based on the impending slippage model of electrode arrays sliding over the endosteum lining are reported in this paper. In this study, friction coefficients of the Nucleus standard straight and the Contour arrays have been determined with and without lubricants applied on the endosteum lining. In the absence of applied lubricants, friction coefficients were found to be 0.19 for the Nucleus standard straight array and 0.12 for the Contour array. Application of lubricants (glycerin and sorbelene) has the potential to lower the friction coefficient for Nucleus standard straight array (0.12 and 0.15) and for the Contour array (0.04 and 0.08). These results are used in finite element models to predict accurately the trajectories of electrode arrays and sliding contact pressures on cochlear structures to evaluate the likelihood of damage sustained during insertion.     

A structure for amplified DNA

We have employed gene transfer to generate cell lines in which a chromosomal region consisting solely of defined DNA sequences has undergone gene amplification. We have analyzed recombinant clones from the amplified array to determine the physical structure of amplified DNA in the cell lines. The amplified DNA we have analyzed consists of a tandem array of at least 20 individual repeating units. The individual units are contiguous, and are joined to one another by homologous recombination between repeated sequences. At first approximation, all homologous recombinations are permitted such that crossing-over may occur between any two repeated sequences. Since individual units contain multiple repeated elements, the array is not a regularly repeating structure. The individual units within the array are heterogeneous, both in size and in sequence content. These observations suggest models of gene amplification which involve multiple cycles of unscheduled DNA replication at a single locus, followed by multiple recombination events which serve to link individual units to one another and ultimately to the chromosome.     

Higher plant cortical microtubule array analyzed in vitro in the presence of the cell wall

Plant morphogenesis depends on an array of microtubules in the cell cortex, the cortical array. Although the cortical array is known to be essential for morphogenesis, it is not known how the array becomes organized or how it functions mechanistically. Here, we report the development of an in vitro model that provides good access to the cortical array while preserving the array's organization and, importantly, its association with the cell wall. Primary roots of maize (Zea mays) are sectioned, without fixation, in a drop of buffer and then incubated as desired before eventual fixation. Sectioning removes cytoplasm except for a residuum comprising cortical microtubules, vesicles, and fragments of plasma membrane underlying the microtubules. The majority of the cortical microtubules remain in the cut-open cells for more than 1 h, fully accessible to the incubation solution. The growth zone or more mature tissue can be sectioned, providing access to cortical arrays that are oriented either transversely or obliquely to the long axis of the root. Using this assay, we report, first, that cortical microtubule stability is regulated by protein phosphorylation; second, that cortical microtubule stability is a function of orientation, with divergent microtubules within the array depolymerizing within minutes of sectioning; and third, that the polarity of microtubules in the cortical array is not uniform. These results suggest that the organization of the cortical array involves random nucleation followed by selective stabilization of microtubules formed at the appropriate orientation, and that the signal specifying alignment must treat orientations of +/- 180 degrees as equivalent.     

A novel approach for increasing sensitivity and correcting saturation artifacts of radioactively labeled cDNA arrays

MOTIVATION: The radioactivity labeled DNA array platform is a robust and accurate way for a high-throughput measurement of gene expression levels in biological samples. Despite its high degree of sensitivity and reproducibility, this platform has several sources of variation. These are related to the presence of saturation effects in the array images and impede the degree of accuracy at which gene expression levels are determined. RESULTS: Here we describe a simple, but effective, approach for combining expression data from a series of autoradiographic exposures of variable length. This technique increases the sensitivity of this array platform by detecting low-expressed genes at longer exposures. It also improves the measurement accuracy of highly abundant genes by considering only values from the linear portion of dependency between the exposure times and gene intensities. As a result, the described approach improves the outcome of the subsequent steps of array data normalization and mining.